Download MendeleyStructural basis for guanidine sensing by the ykkC family of riboswitches.
Battaglia, R.A., Price, I.R., Ke, A.(2017) RNA 23: 578-585
- PubMed: 28096518
- DOI: https://doi.org/10.1261/rna.060186.116
- Primary Citation of Related Structures:
5U3G - PubMed Abstract:
Regulation of gene expression by cis- encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp 2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification-a previously unappreciated aspect of bacterial physiology.
Organizational Affiliation:
Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA.
